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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ), 'gf_id' => 'HOM05D001368', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001368' ), 'data_identifier' => 'HOM05D001368', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001368', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '457', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A03p10890' => 'bna', 'A03p20900' => 'bna', 'A05p08100' => 'bna', 'A05p40150' => 'bna', 'A10p18220' => 'bna', 'Aa31LG1G12910' => 'aar', 'Aa31LG5G18690' => 'aar', 'Aa31LG8G4740' => 'aar', 'Aa31sc88G50' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2774' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_340.354' => 'aag', 'Actinidia07204' => 'ach', 'Actinidia11483' => 'ach', 'Actinidia13160' => 'ach', 'Actinidia20805' => 'ach', 'Actinidia24173' => 'ach', 'Actinidia29012' => 'ach', 'Actinidia32577' => 'ach', 'Ah.01g004670' => 'amhyb', 'Ah.04g159270' => 'amhyb', 'Ah.06g195290' => 'amhyb', 'Ah.12g064400' => 'amhyb', 'AL3G19620' => 'aly', 'AL3G19640' => 'aly', 'AL4G34800' => 'aly', 'AL6G33810' => 'aly', 'AL8G13400' => 'aly', 'Aqoxy1G00007' => 'aox', 'Aqoxy1G00815' => 'aox', 'Aqoxy2G02364' => 'aox', 'Aqoxy5G03801' => 'aox', 'arahy.Tifrunner.gnm1.ann1.085SIZ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.24KS4K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.69Y2E9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F0505K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FMIT1J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H94RDL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IK1H1Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NPHB92' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UJ68TN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.W33KED' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y2PT15' => 'arhy', 'AT2G37860' => 'ath', 'AT3G08630' => 'ath', 'AT3G08640' => 'ath', 'AT5G22790' => 'ath', 'ATR0307G032' => 'atr', 'ATR0559G260' => 'atr', 'Atru.chr3.3403' => 'acertr', 'Atru.chr8.2077' => 'acertr', 'Atru.chr8.65' => 'acertr', 'AUR62000274' => 'cqu', 'AUR62006621' => 'cqu', 'AUR62023964' => 'cqu', 'AUR62024940' => 'cqu', 'AUR62030604' => 'cqu', 'AUR62031764' => 'cqu', 'BcaB01g04694' => 'bca', 'BcaB02g09241' => 'bca', 'BcaB04g21248' => 'bca', 'BcaB05g21534' => 'bca', 'BcaB07g32705' => 'bca', 'BcaB08g36408' => 'bca', 'BcaC01g05588' => 'bca', 'BcaC01g05680' => 'bca', 'BcaC01g05741' => 'bca', 'BcaC01g06568' => 'bca', 'BcaC02g11916' => 'bca', 'BcaC04g19597' => 'bca', 'BcaC09g47980' => 'bca', 'BolC1t05498H' => 'bol', 'BolC3t13325H' => 'bol', 'BolC3t13721H' => 'bol', 'BolC3t14853H' => 'bol', 'BolC4t22606H' => 'bol', 'BolC5t34574H' => 'bol', 'BolC7t45659H' => 'bol', 'BolC9t58259H' => 'bol', 'BraA01t04339Z' => 'bra', 'BraA03t10399Z' => 'bra', 'BraA03t11330Z' => 'bra', 'BraA05t19778Z' => 'bra', 'BraA10t43897Z' => 'bra', 'C03p12530' => 'bna', 'C03p23270' => 'bna', 'C03p24550' => 'bna', 'C04p10030' => 'bna', 'C05p59230' => 'bna', 'C07p51670' => 'bna', 'C09p53830' => 'bna', 'CAN.G1005.4' => 'can', 'CAN.G229.34' => 'can', 'CAN.G644.42' => 'can', 'CAN.G659.18' => 'can', 'CANSAT35G0028' => 'cansat', 'CANSAT55G0001' => 'cansat', 'CANSAT64G0750' => 'cansat', 'CARHR082930' => 'chi', 'CARHR082940' => 'chi', 'CARHR132410' => 'chi', 'CARHR190810' => 'chi', 'Carub.0003s0776' => 'cru', 'Carub.0003s0777' => 'cru', 'Carub.0004s1977' => 'cru', 'Carub.0006s2050' => 'cru', 'Ca_01688_v3' => 'car', 'Ca_07573_v3' => 'car', 'Ca_07791_v3' => 'car', 'Ca_07792_v3' => 'car', 'Ca_26602_v3' => 'car', 'CBR_g31200' => 'cbr', 'CBR_g48677' => 'cbr', 'CBR_g54103' => 'cbr', 'Cc01_g09810' => 'ccan', 'Cc01_g09820' => 'ccan', 'Cc01_g09950' => 'ccan', 'Cc06_g00220' => 'ccan', 'Cc06_g02160' => 'ccan', 'CDE03G0465' => 'cde', 'CDE04G1500' => 'cde', 'CDE04G1641' => 'cde', 'CDE04G3261' => 'cde', 'CDE04G3779' => 'cde', 'CDE07G0789' => 'cde', 'CDE07G0990' => 'cde', 'Cfa010101' => 'cfa', 'Cfa017004' => 'cfa', 'Cfa017310' => 'cfa', 'Ciclev10011995m.g' => 'ccl', 'Ciclev10012066m.g' => 'ccl', 'Ciclev10028580m.g' => 'ccl', 'CiPaw.05G131800' => 'cil', 'CiPaw.09G199900' => 'cil', 'CiPaw.09G223000' => 'cil', 'CiPaw.10G148700' => 'cil', 'CiPaw.10G166200' => 'cil', 'CiPaw.13G142100' => 'cil', 'ClCG02G021810' => 'cla', 'ClCG10G021510' => 'cla', 'COL.COLO4_03909' => 'col', 'COL.COLO4_05676' => 'col', 'COL.COLO4_12154' => 'col', 'COL.COLO4_12157' => 'col', 'COL.COLO4_14714' => 'col', 'COL.COLO4_19273' => 'col', 'Cpa.g.sc0.74' => 'cpa', 'Cpa.g.sc47.45' => 'cpa', 'Cpa.g.sc56.47' => 'cpa', 'Cre02.g141100' => 'cre', 'Cre16.g678000' => 'cre', 'CsaV3_3G034510' => 'csa', 'CsaV3_4G027370' => 'csa', 'CsaV3_6G014600' => 'csa', 'CSS0014376' => 'camsi', 'CSS0027244' => 'camsi', 'CSS0031444' => 'camsi', 'CSS0042307' => 'camsi', 'CSS0044003' => 'camsi', 'DCAR_006503' => 'dca', 'DCAR_011613' => 'dca', 'DCAR_023964' => 'dca', 'DCAR_024053' => 'dca', 'DCAR_028932' => 'dca', 'Dinv16943' => 'din', 'Dinv29410' => 'din', 'Dinv35549' => 'din', 'Dinv37053' => 'din', 'Dinv37054' => 'din', 'Dinv37128' => 'din', 'Duzib093G2226' => 'dzi', 'Duzib128G0291' => 'dzi', 'Duzib133G0807' => 'dzi', 'Duzib133G1402' => 'dzi', 'Duzib151G0515' => 'dzi', 'Duzib168G0059' => 'dzi', 'Duzib212G0729' => 'dzi', 'ECA236G2243' => 'eca', 'ECA236G2626' => 'eca', 'ECA248G0680' => 'eca', 'EL10Ac2g02655' => 'bvu', 'EL10Ac4g10022' => 'bvu', 'EL10Ac9g21054' => 'bvu', 'Eucgr.B02721' => 'egr', 'Eucgr.B03901' => 'egr', 'Eucgr.K01298' => 'egr', 'FAN02G3410' => 'fan', 'FAN02G3941' => 'fan', 'FAN05G3086' => 'fan', 'FAN05G5556' => 'fan', 'FAN09G0370' => 'fan', 'FAN11G3135' => 'fan', 'FAN14G0938' => 'fan', 'FAN16G3298' => 'fan', 'FAN21G4064' => 'fan', 'FAN25G3565' => 'fan', 'FvH4_3g30080' => 'fve', 'FvH4_6g09440' => 'fve', 'FvH4_6g12860' => 'fve', 'Glyma.07G138400' => 'gma', 'Glyma.09G271800' => 'gma', 'Glyma.12G180500' => 'gma', 'Glyma.13G320300' => 'gma', 'Glyma.16G221100' => 'gma', 'Glyma.18G188800' => 'gma', 'Glyma.18G217200' => 'gma', 'Gohir.A01G221400' => 'ghi', 'Gohir.A02G001600' => 'ghi', 'Gohir.A02G001700' => 'ghi', 'Gohir.A09G091900' => 'ghi', 'Gohir.A13G223200' => 'ghi', 'Gohir.D01G210400' => 'ghi', 'Gohir.D02G001900' => 'ghi', 'Gohir.D02G002000' => 'ghi', 'Gohir.D09G091800' => 'ghi', 'Gorai.002G256100' => 'gra', 'Gorai.005G002400' => 'gra', 'Gorai.005G002500' => 'gra', 'Gorai.006G108400' => 'gra', 'Gorai.013G258700' => 'gra', 'GSVIVG01031414001' => 'vvi', 'GSVIVG01034077001' => 'vvi', 'HanXRQChr01g0000421' => 'han', 'HanXRQChr01g0002571' => 'han', 'HanXRQChr06g0179601' => 'han', 'HanXRQChr09g0267511' => 'han', 'HanXRQChr09g0268901' => 'han', 'HanXRQChr11g0320791' => 'han', 'HanXRQChr11g0345091' => 'han', 'HanXRQChr14g0443071' => 'han', 'HanXRQChr14g0451921' => 'han', 'HanXRQChr14g0454871' => 'han', 'Haze_20871' => 'cav', 'Haze_21202' => 'cav', 'Haze_23467' => 'cav', 'Hma1.2p1_0051F.1_g029800' => 'hma', 'Hma1.2p1_0106F.1_g051190' => 'hma', 'Hma1.2p1_0174F.1_g076640' => 'hma', 'Hma1.2p1_1498F.1_g287140' => 'hma', 'HPP92_000655' => 'vpl', 'HPP92_000691' => 'vpl', 'HPP92_008564' => 'vpl', 'HPP92_012616' => 'vpl', 'HPP92_018986' => 'vpl', 'Hund00799' => 'sun', 'Hund11324' => 'sun', 'Hund14495' => 'sun', 'Lalb_Chr01g0023941' => 'lal', 'Lalb_Chr03g0042571' => 'lal', 'Lalb_Chr03g0043851' => 'lal', 'Lalb_Chr07g0195781' => 'lal', 'Lalb_Chr19g0125131' => 'lal', 'Lalb_Chr22g0350561' => 'lal', 'Lj1C218T7' => 'lonja', 'Lj1g0012528' => 'lja', 'Lj1g0016877' => 'lja', 'Lj3A962T51' => 'lonja', 'Lj3E939T1' => 'lonja', 'Lj3g0008079' => 'lja', 'Lj3g0010561' => 'lja', 'Lsat_1_v5_gn_2_96641' => 'lsa', 'Lsat_1_v5_gn_5_151420' => 'lsa', 'Lsat_1_v5_gn_8_110401' => 'lsa', 'Manes.08G168200' => 'mes', 'Manes.09G097000' => 'mes', 'Manes.09G121900' => 'mes', 'Manes.11G155600' => 'mes', 'Mapoly0019s0041' => 'mpo', 'Mapoly0083s0092' => 'mpo', 'MBI05_g02652_MAGBIO' => 'mbi', 'MBI14_g08996_MAGBIO' => 'mbi', 'MBI15_g16010_MAGBIO' => 'mbi', 'MBI19_g15082_MAGBIO' => 'mbi', 'MCO05G396' => 'mco', 'MCO07G336' => 'mco', 'MD03G1132600' => 'mdo', 'MD04G1137400' => 'mdo', 'MD04G1177700' => 'mdo', 'MD07G1117800' => 'mdo', 'MD11G1154900' => 'mdo', 'MD12G1193000' => 'mdo', 'Medtr2g084605' => 'mtr', 'Medtr7g064130' => 'mtr', 'Medtr7g064190' => 'mtr', 'Medtr7g074070' => 'mtr', 'Medtr7g074090' => 'mtr', 'MELO3C009222.2' => 'cme', 'MELO3C021464.2' => 'cme', 'MELO3C025256.2' => 'cme', 'Migut.D02324' => 'egut', 'Migut.J00274' => 'egut', 'Migut.J00560' => 'egut', 'Migut.L01530' => 'egut', 'MSTRG.18718' => 'ama', 'MSTRG.19058' => 'ama', 'MSTRG.19485' => 'ama', 'Nitab4.5_0000362g0100' => 'nta', 'Nitab4.5_0000442g0220' => 'nta', 'Nitab4.5_0001215g0120' => 'nta', 'Nitab4.5_0001876g0010' => 'nta', 'Nitab4.5_0002571g0070' => 'nta', 'Nitab4.5_0006423g0020' => 'nta', 'Nitab4.5_0007589g0020' => 'nta', 'Nitab4.5_0008207g0050' => 'nta', 'Nitab4.5_0011665g0020' => 'nta', 'Nn2g11270' => 'nnu', 'Nn7g37268' => 'nnu', 'Nn7g37269' => 'nnu', 'Nn7g37469' => 'nnu', 'Oeu007823.1' => 'oeu', 'Oeu023728.2' => 'oeu', 'Oeu053776.1' => 'oeu', 'Os01g0812900' => 'osa', 'Os03g0390900' => 'osa', 'Os04g0524400' => 'osa', 'Os07g0240300' => 'osa', 'Os11g0432800' => 'osa', 'Peaxi162Scf00318g00316' => 'pax', 'Peaxi162Scf00318g00320' => 'pax', 'Peaxi162Scf00374g00033' => 'pax', 'Peaxi162Scf00732g00133' => 'pax', 'Peaxi162Scf00789g00212' => 'pax', 'PGR004G2868' => 'pgr', 'PGR031G2025' => 'pgr', 'PGR102G0092' => 'pgr', 'PGR102G3113' => 'pgr', 'PGSC0003DMG400000435' => 'stu', 'PGSC0003DMG400006564' => 'stu', 'PGSC0003DMG400024261' => 'stu', 'PGSC0003DMG400027703' => 'stu', 'Phvul.005G128300' => 'pvu', 'Phvul.008G079300' => 'pvu', 'Phvul.008G114600' => 'pvu', 'Phvul.010G059300' => 'pvu', 'Potri.006G111300' => 'ptr', 'Potri.009G150400' => 'ptr', 'Potri.016G103100' => 'ptr', 'Potri.016G140700' => 'ptr', 'Pp3c11_2790' => 'ppa', 'Pp3c2_21600' => 'ppa', 'Pp3c2_34630' => 'ppa', 'Pp3c4_25760' => 'ppa', 'Pp3c7_21310' => 'ppa', 'PRCOL_00001641' => 'pco', 'PRCOL_00002262' => 'pco', 'PRCOL_00003745' => 'pco', 'PRCOL_00007098' => 'pco', 'Prupe.3G101300' => 'ppe', 'Prupe.6G117100' => 'ppe', 'Prupe.6G169100' => 'ppe', 'Prupe.6G263400' => 'ppe', 'Prupe.6G297600' => 'ppe', 'Psat3g117120' => 'psa', 'Psat3g117160' => 'psa', 'Psat3g133000' => 'psa', 'Psat5g254080' => 'psa', 'PSO210G6197' => 'pso', 'PSO339G6381' => 'pso', 'PSO384G4003' => 'pso', 'PSO478G4388' => 'pso', 'PSO541G3390' => 'pso', 'PSO675G2144' => 'pso', 'PSO782G3471' => 'pso', 'PSO832G3380' => 'pso', 'QL01p014032' => 'qlo', 'QL07p004779' => 'qlo', 'QL07p004792' => 'qlo', 'QL07p028553' => 'qlo', 'QL07p031279' => 'qlo', 'QL07p031623' => 'qlo', 'RcHm_v2.0_Chr3g0459911' => 'rch', 'RcHm_v2.0_Chr3g0464891' => 'rch', 'RcHm_v2.0_Chr5g0055771' => 'rch', 'Rhsim04G0162800' => 'rsi', 'Rhsim05G0233200' => 'rsi', 'Rhsim13G0104400' => 'rsi', 'Sabra04G0157200' => 'sbr', 'Sabra06G0086500' => 'sbr', 'Sabra09G0119100' => 'sbr', 'Sabra16G0102900' => 'sbr', 'SalBow5G0484' => 'sbo', 'SalBow6G1663' => 'sbo', 'SalBow6G5450' => 'sbo', 'Sc01g0004720' => 'sci', 'Sc20g0007220' => 'sci', 'Sc21g0004630' => 'sci', 'Sed0001093' => 'sed', 'Sed0004297' => 'sed', 'Sed0006115' => 'sed', 'Sed0010132' => 'sed', 'Sed0012466' => 'sed', 'Sed0027132' => 'sed', 'SEGI_04502' => 'sgi', 'SEGI_23964' => 'sgi', 'SEGI_32198' => 'sgi', 'SEGI_34489' => 'sgi', 'SGA_v2.0_scaffold192G40636' => 'sas', 'SGA_v2.0_scaffold193G40718' => 'sas', 'SGA_v2.0_scaffold21G09444' => 'sas', 'SGA_v2.0_scaffold75G24972' => 'sas', 'SHI12948' => 'shi', 'SMO116G0197' => 'smo', 'SMO143G0172' => 'smo', 'SMO164G0089' => 'smo', 'Solyc09g011340.3' => 'sly', 'Solyc09g031940.1' => 'sly', 'Solyc10g074880.3' => 'sly', 'Solyc11g066740.2' => 'sly', 'Sopen09g006060' => 'spe', 'Sopen09g014410' => 'spe', 'Sopen10g027370' => 'spe', 'Sopen11g026480' => 'spe', 'Sp3g07080' => 'spa', 'Sp4g20170' => 'spa', 'Sp6g22640' => 'spa', 'SpUn1555_0010' => 'spa', 'TAR623G0826' => 'tar', 'TAR633G1378' => 'tar', 'TAR633G2110' => 'tar', 'TAR636G0613' => 'tar', 'THA.LOC104810892' => 'tha', 'THA.LOC104820495' => 'tha', 'THA.LOC104823332' => 'tha', 'THA.LOC104824523' => 'tha', 'Thecc.04G148000' => 'tca', 'Thecc.05G030600' => 'tca', 'Thecc.09G293400' => 'tca', 'Thhalv10013586m.g' => 'esa', 'Thhalv10016685m.g' => 'esa', 'Thhalv10021063m.g' => 'esa', 'Thhalv10021092m.g' => 'esa', 'TPR.G24332' => 'tpr', 'TPR.G24338' => 'tpr', 'TPR.G27950' => 'tpr', 'TPR.G32381' => 'tpr', 'TWI53G1520' => 'twi', 'TWI74G0003' => 'twi', 'TWI74G1104' => 'twi', 'TWI74G1600' => 'twi', 'TWI75G1844' => 'twi', 'TWI77G0028' => 'twi', 'TWI77G0491' => 'twi', 'unitig_0.g961' => 'ugi', 'unitig_747.g21967' => 'ugi', 'unitig_749.g14231' => 'ugi', 'vmacro03227' => 'vma', 'vmacro08630' => 'vma', 'vmacro11971' => 'vma', 'vmacro23024' => 'vma', 'VMungo0331G1435' => 'vmu', 'VMungo1080G1333' => 'vmu', 'VMungo1383G0432' => 'vmu', 'VMungo1383G0666' => 'vmu', 'Zm00001eb076950' => 'zma', 'Zm00001eb128660' => 'zma', 'Zm00001eb150040' => 'zma', 'Zm00001eb303990' => 'zma', 'Zm00001eb369170' => 'zma' ) $gf_id = 'HOM05D001368' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001368' ) $data_identifier = 'HOM05D001368' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 12, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 4, 'arhy' => (int) 11, 'ath' => (int) 4, 'atr' => (int) 2, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 13, 'bol' => (int) 8, 'bra' => (int) 5, 'can' => (int) 4, 'cansat' => (int) 3, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 5, 'cbr' => (int) 3, 'ccan' => (int) 5, 'cde' => (int) 7, 'cfa' => (int) 3, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 2, 'col' => (int) 6, 'cpa' => (int) 3, 'cre' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 10, 'fve' => (int) 3, 'gma' => (int) 7, 'ghi' => (int) 9, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 10, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 5, 'sun' => (int) 3, 'lal' => (int) 6, 'lonja' => (int) 3, 'lja' => (int) 4, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 2, 'mbi' => (int) 4, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 9, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 5, 'pax' => (int) 5, 'pgr' => (int) 4, 'stu' => (int) 4, 'pvu' => (int) 4, 'ptr' => (int) 4, 'ppa' => (int) 5, 'pco' => (int) 4, 'ppe' => (int) 5, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 3, 'sci' => (int) 3, 'sed' => (int) 6, 'sgi' => (int) 4, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 3, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 4, 'tar' => (int) 4, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 4, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 3, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb369170' $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